NAME

       bio-vcf - domain specific language (DSL) for processing the VCF format

SYNOPSIS

       bio-vcf [options] filename

DESCRIPTION

       bio-vcf 0.9.5 (biogem Ruby 2.7.2 with pcows) by Pjotr Prins 2015-2020

       e.g.  bio-vcf < test/data/input/somaticsniper.vcf

       -i, --ignore-missing
              Ignore missing data

       --filter cmd
              Evaluate filter on each record

       --sfilter cmd
              Evaluate filter on each sample

       --sfilter-samples list
              Filter on selected samples (e.g., 0,1

       --ifilter, --if cmd
              Include filter

       --ifilter-samples list
              Include set - implicitely defines exclude set

       --efilter, --ef cmd
              Exclude filter

       --efilter-samples list
              Exclude set - overrides exclude set

       --add-filter name
              Set/add filter field to name

       --bed bedfile
              Filter on BED elements

       -e, --eval cmd
              Evaluate command on each record

       --eval-once cmd
              Evaluate command once (usually for header info)

       --seval cmd
              Evaluate command on each sample

       --rewrite eval
              Rewrite INFO

       --samples list
              Output selected samples

       --rdf  Generate Turtle RDF (also check out --template!)

       --num-threads [num]
              Multi-core version (default ALL)

       --thread-lines num
              Fork thread on num lines (default 40000)

       --skip-header
              Do not output VCF header info

       --set-header list
              Set a special tab delimited output header (#samples expands to sample names)

       -t, --template erb
              Use ERB template for output

       --add-header-tag
              Add bio-vcf status tag to header output

       --timeout [num]
              Timeout waiting for thread to complete (default 180)

       --names
              Output sample names

       --statistics
              Output statistics

       -q, --quiet
              Run quietly

       -v, --verbose
              Run verbosely

       --debug
              Show debug messages and keep intermediate output

       --id name
              Identifier

       --tags list
              Add tags

       -h, --help
              display this help and exit

       Vcf parser

AUTHOR

        This manpage was written by Nilesh Patra for the Debian distribution and
        can be used for any other usage of the program.